FIMO (Find Individual Motif Occurrences) is a software tool designed to scan DNA or protein sequences for occurrences of motifs described by position-specific scoring matrices. The program computes log-likelihood ratio scores for each position in the sequence, converts these scores to P-values using dynamic programming, and estimates q-values for false discovery rates. FIMO outputs results in various formats, including HTML, XML, and formats suitable for the UCSC Genome Browser. It is part of the MEME Suite and can be used in conjunction with other motif-based sequence analysis tools. FIMO is efficient, capable of scanning DNA sequences at a rate of 3.5 Mb/s on a single CPU. The tool is particularly useful for identifying individual candidate binding sites or protein motifs and has been demonstrated to effectively identify CTCF binding sites in the human genome, with a precision–recall curve suggesting high enrichment of predicted sites at the top of the list.FIMO (Find Individual Motif Occurrences) is a software tool designed to scan DNA or protein sequences for occurrences of motifs described by position-specific scoring matrices. The program computes log-likelihood ratio scores for each position in the sequence, converts these scores to P-values using dynamic programming, and estimates q-values for false discovery rates. FIMO outputs results in various formats, including HTML, XML, and formats suitable for the UCSC Genome Browser. It is part of the MEME Suite and can be used in conjunction with other motif-based sequence analysis tools. FIMO is efficient, capable of scanning DNA sequences at a rate of 3.5 Mb/s on a single CPU. The tool is particularly useful for identifying individual candidate binding sites or protein motifs and has been demonstrated to effectively identify CTCF binding sites in the human genome, with a precision–recall curve suggesting high enrichment of predicted sites at the top of the list.